Zinc in PDB 5tt8: Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide

The structure of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide, PDB code: 5tt8 was solved by J.K.Modak, A.Roujeinikova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.32 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.240, 134.400, 165.280, 90.00, 90.04, 90.00
R / Rfree (%)	19.8 / 23.1

The structure of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide (pdb code 5tt8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide, PDB code: 5tt8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:43.4 occ:0.70 ND1 A:HIS129 1.8 33.8 1.0 N4 A:D8W303 1.9 35.6 1.0 NE2 A:HIS110 1.9 29.3 1.0 NE2 A:HIS112 2.0 30.2 1.0 CD2 A:HIS110 2.6 32.2 1.0 CE1 A:HIS129 2.7 28.7 1.0 CD2 A:HIS112 2.8 35.3 1.0 O4 A:D8W303 2.9 29.6 1.0 S3 A:D8W303 2.9 37.7 1.0 CG A:HIS129 2.9 32.0 1.0 CE1 A:HIS110 3.1 30.6 1.0 CE1 A:HIS112 3.2 32.4 1.0 CB A:HIS129 3.4 32.7 1.0 OG1 A:THR191 3.7 39.8 1.0 CG A:HIS110 3.8 35.0 1.0 NE2 A:HIS129 3.9 34.2 1.0 CD2 A:HIS129 4.0 33.1 1.0 C8 A:D8W303 4.0 30.7 1.0 ND1 A:HIS110 4.0 35.0 1.0 CG A:HIS112 4.1 33.2 1.0 O3 A:D8W303 4.1 38.6 1.0 ND1 A:HIS112 4.2 33.8 1.0 S2 A:D8W303 4.8 41.3 1.0 OE1 A:GLU116 4.9 34.5 1.0 CA A:HIS129 4.9 35.3 1.0 N3 A:D8W303 4.9 32.5 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:37.9 occ:1.00 NE2 B:HIS112 1.9 36.1 1.0 NE2 B:HIS110 1.9 33.5 1.0 N4 B:D8W303 2.1 29.9 1.0 CE1 B:HIS112 2.2 38.8 1.0 ND1 B:HIS129 2.4 34.2 1.0 CD2 B:HIS110 2.8 34.0 1.0 O4 B:D8W303 3.0 42.0 1.0 CE1 B:HIS110 3.0 37.8 1.0 S3 B:D8W303 3.1 31.1 1.0 CD2 B:HIS112 3.2 35.1 1.0 CG B:HIS129 3.3 34.5 1.0 CE1 B:HIS129 3.4 30.1 1.0 ND1 B:HIS112 3.4 38.3 1.0 CB B:HIS129 3.5 40.1 1.0 CG B:HIS112 3.9 38.0 1.0 C8 B:D8W303 4.0 30.4 1.0 OG1 B:THR191 4.0 30.8 1.0 CG B:HIS110 4.0 41.4 1.0 ND1 B:HIS110 4.1 34.6 1.0 O3 B:D8W303 4.3 34.8 1.0 CD2 B:HIS129 4.5 27.7 1.0 NE2 B:HIS129 4.5 24.8 1.0 OE1 B:GLU116 4.5 28.8 1.0 S2 B:D8W303 4.7 37.4 1.0 N3 B:D8W303 4.9 31.3 1.0 CA B:HIS129 5.0 36.2 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:28.1 occ:1.00 NE2 C:HIS110 2.1 21.2 1.0 NE2 C:HIS112 2.2 21.7 1.0 N4 C:D8W303 2.2 28.3 1.0 CD2 C:HIS110 2.4 19.9 1.0 ND1 C:HIS129 2.4 20.3 1.0 CE1 C:HIS112 3.0 20.1 1.0 CD2 C:HIS112 3.0 18.8 1.0 O4 C:D8W303 3.2 15.2 1.0 S3 C:D8W303 3.3 25.3 1.0 CE1 C:HIS129 3.4 17.7 1.0 CE1 C:HIS110 3.4 19.2 1.0 CG C:HIS129 3.4 18.3 1.0 CB C:HIS129 3.7 19.3 1.0 CG C:HIS110 3.7 19.4 1.0 OG1 C:THR191 3.8 23.9 1.0 ND1 C:HIS112 4.0 18.9 1.0 O2 C:GOL304 4.0 24.5 1.0 CG C:HIS112 4.0 16.6 1.0 ND1 C:HIS110 4.1 17.5 1.0 C8 C:D8W303 4.2 18.3 1.0 O3 C:D8W303 4.5 25.1 1.0 NE2 C:HIS129 4.5 18.6 1.0 CD2 C:HIS129 4.5 17.2 1.0 C2 C:GOL304 4.8 19.4 1.0 CB C:HIS110 4.9 22.2 1.0 CG2 C:THR191 5.0 18.4 1.0 CB C:THR191 5.0 20.5 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:41.7 occ:0.70 NE2 D:HIS112 1.9 43.6 1.0 N4 D:D8W302 1.9 26.1 1.0 NE2 D:HIS110 2.0 42.0 1.0 O4 D:D8W302 2.7 44.1 1.0 CD2 D:HIS110 2.7 39.9 1.0 S3 D:D8W302 2.8 37.1 1.0 CD2 D:HIS112 2.9 40.2 1.0 ND1 D:HIS129 2.9 46.2 1.0 CE1 D:HIS112 2.9 45.9 1.0 CE1 D:HIS110 3.2 41.3 1.0 CE1 D:HIS129 3.7 52.5 1.0 CG D:HIS129 3.7 44.9 1.0 OG1 D:THR191 3.7 31.0 1.0 C8 D:D8W302 3.8 30.9 1.0 OE2 D:GLU116 3.9 48.1 1.0 CB D:HIS129 4.0 40.7 1.0 CG D:HIS110 4.0 38.1 1.0 ND1 D:HIS112 4.0 52.4 1.0 CG D:HIS112 4.0 44.5 1.0 O3 D:D8W302 4.1 37.0 1.0 ND1 D:HIS110 4.2 39.1 1.0 S2 D:D8W302 4.5 47.4 1.0 NE2 D:HIS129 4.6 53.8 1.0 CD2 D:HIS129 4.7 45.1 1.0 CD D:GLU116 4.7 48.5 1.0 N3 D:D8W302 4.8 35.5 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:40.7 occ:1.00 NE2 E:HIS112 1.7 26.5 1.0 NE2 E:HIS110 1.8 24.3 1.0 N4 E:D8W303 2.2 29.9 0.5 N4 E:D8W303 2.2 29.9 0.5 ND1 E:HIS129 2.3 21.3 1.0 O3 E:D8W303 2.5 27.3 0.5 O3 E:D8W303 2.5 27.4 0.5 CE1 E:HIS112 2.5 21.2 1.0 CD2 E:HIS110 2.7 20.9 1.0 S3 E:D8W303 2.8 27.9 0.5 CD2 E:HIS112 2.8 22.4 1.0 S3 E:D8W303 2.8 27.6 0.5 CE1 E:HIS110 2.9 24.3 1.0 CE1 E:HIS129 3.1 22.2 1.0 CG E:HIS129 3.2 23.9 1.0 CB E:HIS129 3.6 22.4 1.0 ND1 E:HIS112 3.7 26.3 1.0 CG E:HIS112 3.8 22.3 1.0 CG E:HIS110 3.9 18.5 1.0 C8 E:D8W303 3.9 34.0 0.5 C8 E:D8W303 3.9 34.0 0.5 OG1 E:THR191 3.9 29.0 1.0 ND1 E:HIS110 3.9 25.1 1.0 OE1 E:GLU116 4.0 30.3 1.0 O4 E:D8W303 4.0 29.0 0.5 O4 E:D8W303 4.1 29.0 0.5 NE2 E:HIS129 4.2 22.7 1.0 CD2 E:HIS129 4.3 25.0 1.0 S2 E:D8W303 4.6 61.3 0.5 S2 E:D8W303 4.6 62.1 0.5 CD E:GLU116 4.9 22.1 1.0 N3 E:D8W303 4.9 33.4 0.5 N3 E:D8W303 4.9 33.4 0.5

Zinc binding site 6 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:46.7 occ:0.70 NE2 F:HIS112 1.9 46.2 1.0 NE2 F:HIS110 2.0 43.2 1.0 CD2 F:HIS110 2.4 39.9 1.0 CE1 F:HIS112 2.8 50.0 1.0 CD2 F:HIS112 2.9 47.5 1.0 CB F:HIS129 3.0 34.9 1.0 CE1 F:HIS110 3.2 35.3 1.0 ND1 F:HIS129 3.3 43.1 1.0 CG F:HIS129 3.4 38.5 1.0 CG F:HIS110 3.7 41.3 1.0 ND1 F:HIS112 3.9 48.8 1.0 CG F:HIS112 3.9 48.1 1.0 ND1 F:HIS110 4.0 37.9 1.0 CA F:HIS129 4.3 34.6 1.0 CE1 F:HIS129 4.4 46.0 1.0 CG2 F:THR191 4.5 39.6 1.0 O F:HIS129 4.6 36.5 1.0 CD2 F:HIS129 4.7 43.4 1.0 N F:HIS129 4.7 33.7 1.0 O F:HIS110 4.8 39.0 1.0 OE1 F:GLU116 4.8 43.5 1.0 C F:HIS129 4.9 32.1 1.0 CB F:HIS110 5.0 38.9 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn301 b:48.3 occ:1.00 NE2 G:HIS112 1.8 30.6 1.0 NE2 G:HIS110 1.8 32.8 1.0 N4 G:D8W302 2.0 26.7 1.0 ND1 G:HIS129 2.5 46.1 1.0 CD2 G:HIS112 2.7 33.6 1.0 CD2 G:HIS110 2.7 34.6 1.0 CE1 G:HIS112 2.9 32.6 1.0 CE1 G:HIS110 3.0 31.0 1.0 S3 G:D8W302 3.1 33.3 1.0 O4 G:D8W302 3.1 23.8 1.0 CG G:HIS129 3.4 45.8 1.0 CE1 G:HIS129 3.5 40.7 1.0 CB G:HIS129 3.6 41.0 1.0 CG G:HIS112 3.9 33.9 1.0 CG G:HIS110 3.9 37.9 1.0 ND1 G:HIS112 3.9 30.8 1.0 ND1 G:HIS110 4.0 32.2 1.0 C8 G:D8W302 4.1 34.9 1.0 OE1 G:GLU116 4.1 30.5 1.0 OG1 G:THR191 4.1 37.8 1.0 O3 G:D8W302 4.3 33.3 1.0 CD2 G:HIS129 4.6 45.1 1.0 NE2 G:HIS129 4.6 43.9 1.0 S2 G:D8W302 4.8 48.8 1.0 CD G:GLU116 4.9 26.5 1.0 N3 G:D8W302 5.0 35.0 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:37.7 occ:1.00 NE2 H:HIS110 1.7 23.9 1.0 NE2 H:HIS112 1.8 31.2 1.0 N4 H:D8W302 1.9 25.3 1.0 ND1 H:HIS129 2.1 25.2 1.0 CD2 H:HIS110 2.5 27.9 1.0 CE1 H:HIS112 2.7 33.1 1.0 CE1 H:HIS110 2.8 28.9 1.0 CD2 H:HIS112 2.9 32.4 1.0 O3 H:D8W302 2.9 27.2 1.0 S3 H:D8W302 2.9 27.4 1.0 CE1 H:HIS129 3.0 27.1 1.0 CG H:HIS129 3.2 22.9 1.0 CB H:HIS129 3.6 29.6 1.0 CG H:HIS110 3.7 30.5 1.0 OG1 H:THR191 3.7 30.3 1.0 ND1 H:HIS112 3.8 31.3 1.0 ND1 H:HIS110 3.8 30.3 1.0 CG H:HIS112 4.0 31.6 1.0 C8 H:D8W302 4.0 31.6 1.0 NE2 H:HIS129 4.1 22.3 1.0 O4 H:D8W302 4.2 29.4 1.0 CD2 H:HIS129 4.2 23.1 1.0 OE1 H:GLU116 4.3 26.3 1.0 S2 H:D8W302 4.7 51.1 1.0 N3 H:D8W302 4.9 27.3 1.0

J.K.Modak, Y.C.Liu, C.T.Supuran, A.Roujeinikova. Structure-Activity Relationship For Sulfonamide Inhibition of Helicobacter Pylori Alpha-Carbonic Anhydrase. J. Med. Chem. V. 59 11098 2016.
ISSN: ISSN 1520-4804
PubMed: 28002963
DOI: 10.1021/ACS.JMEDCHEM.6B01333